at OpenHelix

What’s The Answer: (have we improved?)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s highlighted question is something that amused me. In response to that rant about leaving bioinformatics that’s been going around, a thread developed about the reality of the state of bioinformatics today. It amused me because the youngsters have no idea what we were dealing with in the 90s. Those of you who are old-timers like me will remember a lot of the members of this list of Pedro’s Tools–which was the peak of the field and the best collection at the time. Heh.

The recent popularity of the article discussed here has led me to debate what many of my pure computer science friends see as big problems in bioinformatics—poor code quality, lack of testing and documentation, and unreliability. I said that things generally seem to be getting better over time, but they said they keep hearing about vague “improvement” in bioinformatics with no concrete examples.

As just an undergrad (in CS and Molecular Biology) with a short history in the field, I couldn’t come up with much to say. So I turn to you.

Can you give any specific examples of how bioinformatics has improved over time? From specific tools and file formats to general practices?